Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
tcgabiolinks
•
reset
0
votes
1
reply
196
views
combining raw counts and estimated counts
RNASeqData
GEO
TCGAbiolinks
updated 5 weeks ago by
O'Brien
• 0 • written 5 weeks ago by
Noor
• 0
0
votes
7
replies
1.0k
views
How should I know which platforms are available for TCGA methylation?
TCGAbiolinks
updated 3 months ago by
James W. MacDonald
67k • written 3 months ago by
xiaofeiwang198266
• 0
3
votes
3
replies
3.7k
views
maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicatedVariants, : missing required fields from MAF: Chromosome
software error
maftools
tcgabiolinks
updated 10 months ago by
snijesh
▴ 200 • written 7.3 years ago by
Ramiro Magno
▴ 100
0
votes
0
replies
437
views
TCGAbiolinks STAD project 450k Methylation Beta Value data
MethylationArray
normalize450K
TCGAbiolinks
Normalization
MethylationArrayData
11 months ago • updated 10 months ago
Giovanni Calice
▴ 160
0
votes
0
replies
479
views
GDC slides download
TCGAbiolinks
11 months ago
jain72744
• 0
0
votes
4
replies
707
views
I need to calculate the survival rate of TCGA databases
TCGAbiolinks
Survival
updated 11 months ago by
Lluís Revilla Sancho
▴ 760 • written 11 months ago by
tirordep
• 0
0
votes
0
replies
480
views
champ.load() from .idat files of GDC/TCGA dataset
TCGAbiolinks
ChAMP
12 months ago
Thalita
• 0
0
votes
1
reply
919
views
Problems when running GDC_prepare in R
TCGAbiolinks
error
GDC_prepare
15 months ago
leon
• 0
0
votes
0
replies
429
views
Where/how are TCGAbiolinks colData column names sourced from?
clinical
TCGAbiolinks
19 months ago
BioInfoBeginnerrr
• 0
4
votes
8
replies
1.6k
views
TCGAbiolinks cannot find bcr_patient_barcode
TCGAbiolinks
20 months ago
Habil Zare
▴ 200
0
votes
2
replies
1.3k
views
RPPA data (Proteomics analysis)
TCGAbiolinks
limma
22 months ago • updated 21 months ago
qiz218591
• 0
1
vote
1
reply
1.1k
views
Error when running getGDCprojects()
TCGAbiolinks
23 months ago
DevelopingHippo
• 0
2
votes
1
reply
963
views
How to identify the batch informations from the sample ID?
TCGAbiolinks
BatchQC
BatchEffect
updated 17 months ago by
wrab425
• 0 • written 23 months ago by
snijesh
▴ 200
0
votes
0
replies
948
views
KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
Survival
TCGAbiolinks
R
PAAD
23 months ago
Manav
• 0
1
vote
2
replies
2.1k
views
Error when running GDC_prepare
TCGAbiolinks
23 months ago
DevelopingHippo
• 0
1
vote
3
replies
1.3k
views
Some discrepancy between ED genes in cBioPortal vs DESeq2
DESeq2
TCGAbiolinks
2.1 years ago
Alexandre
• 0
0
votes
0
replies
670
views
TCGAbiolinks GDCprepare produces error in vectbl_as_col_location()
TCGAbiolinks
2.3 years ago
lescano
▴ 10
0
votes
0
replies
902
views
Query on TCGA
TCGAbiolinks
TCGAWorkflow
2.4 years ago
hemangininaik09
• 0
0
votes
2
replies
2.0k
views
Error with TCGA package - TCGAbiolinks
TCGAbiolinks
RNASeq
CancerData
updated 2.5 years ago by
Tiago C. Silva
▴ 270 • written 2.6 years ago by
JAcky
• 0
0
votes
0
replies
1.0k
views
About normalization of the datasets from Harmonized TCGA data
TCGAbiolinks
Proteomics
GENOMICS
bioinformatics
2.5 years ago
qiz218591
• 0
0
votes
0
replies
722
views
TCGAbiolinks file.type argument
TCGAbiolinks
2.5 years ago
Elizabeth
• 0
0
votes
0
replies
708
views
Merging two SummarizedExperiment dataesets after downloading using TCGAbiolinks
TCGAbiolinks
TCGAbiolinksGUI.data
SummarizedExperiment
2.7 years ago
syednajeebashraf
• 0
5
votes
4
replies
3.6k
views
HTSeq Counts no longer available
TCGAbiolinks
updated 2.7 years ago by
swbarnes2
★ 1.4k • written 2.8 years ago by
vm
▴ 30
0
votes
4
replies
1.4k
views
GDCdownload Directory Problem :(
TCGAWorkflowData
TCGAbiolinks
updated 11 months ago by
Marcel Ramos
700 • written 2.8 years ago by
Emre
• 0
0
votes
2
replies
2.4k
views
GDCprepare error in TARGET-AML data access
TCGAbiolinks
TARGET-AML
updated 2.8 years ago by
Tiago C. Silva
▴ 270 • written 2.8 years ago by
Лиза
• 0
0
votes
1
reply
2.2k
views
GDCprepare of STAR - counts
GeneExpression
TCGAbiolinks
updated 2.4 years ago by
Aurora
• 0 • written 2.8 years ago by
mahsa
• 0
3
votes
2
replies
2.6k
views
Difference in TCGA RNAseq expression values between GDC harmonized and legacy data
GDC
TCGA
tcgabiolinks
updated 2.8 years ago by
cute scientist
• 0 • written 6.2 years ago by
Antonio Ahn
▴ 10
4
votes
5
replies
1.9k
views
GDCprepare() can never complete request ("Error: cannot allocate vector")
TCGAbiolinks
TCGA
updated 2.8 years ago by
biologsr
• 0 • written 4.4 years ago by
aush
▴ 40
0
votes
0
replies
817
views
GDCquery error when querying mutect2 data
TCGAbiolinks
2.8 years ago
komal.rathi
▴ 120
0
votes
2
replies
2.5k
views
GDCprepare() - R Session Aborted
TCGAbiolinks
R
GDCprepare()
2.8 years ago • updated 2.3 years ago
spyrouglykeria
• 0
6
votes
3
replies
3.6k
views
GDCprepare of RNAseq counts produces error
TCGAbiolinks
updated 2.8 years ago by
Nikolas
• 0 • written 2.8 years ago by
lescano
▴ 10
2
votes
8
replies
6.0k
views
GDCquery_Maf error
TCGAbiolinks
GDCquery_Maf
updated 2.5 years ago by
1526466763
• 0 • written 2.9 years ago by
e.iich
• 0
0
votes
0
replies
1.0k
views
Compare TCGA-PAAD with GTEx gene expression
TCGAbiolinks
3.1 years ago
constantinosdem
• 0
0
votes
0
replies
937
views
TCGAAnalyze_DEA Issue, "Error in names"
miRNAseq
TCGAbiolinks
TCGAAnalyze_DEA
3.2 years ago
Gandino
• 0
0
votes
1
reply
2.7k
views
How to remove duplicate files per case in TCGAbiolonks
TCGAbiolinks
3.2 years ago
raf4
▴ 30
1
vote
2
replies
1.5k
views
Difficulty dowloading hg38 cnv data in tcgabiolinks
TCGAbiolinks
cnv
3.3 years ago • updated 3.2 years ago
raf4
▴ 30
0
votes
1
reply
1.8k
views
pre-proccessing of TCGA data for WGCNA
TCGAbiolinks
WGCNA
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
txtbookir
• 0
0
votes
0
replies
974
views
DEGs for legacy and harmonized dataset
#DEGs
#legacydataset
#harmonizeddataset
TCGAbiolinks
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
Gisele
• 0
0
votes
1
reply
1.4k
views
Help With TCGAbiolinks package
TCGAbiolinks
data
normalize
l
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 years ago by
DANIELA
• 0
0
votes
2
replies
1.5k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGAbiolinks
3.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
2.0k
views
TCGA-BRCA downloading issue by GDCquery
TCGAbiolinks
TCGAWorkflowData
3.7 years ago
H. Z. Amini
▴ 10
0
votes
0
replies
961
views
Determine whether RNAseq data from TCGA is paired or single-end?
TCGA
TCGAbiolinks
3.7 years ago
rebeliscu
• 0
0
votes
3
replies
1.2k
views
discrepancy in number of samples
TCGAquery_recount2
TCGAbiolinks
3.8 years ago
xiaofeiwang18266
▴ 50
1
vote
1
reply
1.7k
views
Does DESeq2 need "scale_counts" for GTEx and TCGA data from recount2 (TCGAquery_recount2)?
TCGAbiolinks
RECOUNT2
DESeq2
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
xiaofeiwang18266
▴ 50
3
votes
8
replies
4.1k
views
error reading from connection (Error in load(url(con)))
TCGAbiolinks
3.8 years ago
xiaofeiwang18266
▴ 50
0
votes
0
replies
1.0k
views
Job:
Postdoc in computational cancer biology at IEO, Milan, Italy
TCGAbiolinks
BiomedicalInformatics
Network
3.9 years ago
martin.schaefer
• 0
0
votes
1
reply
1.0k
views
library(TCGAbiolinks)
TCGAbiolinks
updated 4.0 years ago by
Kevin Blighe
★ 4.0k • written 4.0 years ago by
1664424607
• 0
0
votes
1
reply
2.2k
views
TCGAbiolinks connection error for GDCquery
MethylationArray
TCGAbiolinks
4.1 years ago • updated 4.0 years ago
Sophie Marion de Proce
• 0
0
votes
1
reply
1.2k
views
Error in query for Genomics Data Commons
TCGAbiolinks
updated 4.1 years ago by
shepherl
4.1k • written 4.1 years ago by
sbetrosian
• 0
0
votes
5
replies
3.0k
views
TCGA: to extract clinical data from barcode
cancer
TCGAbiolinks
updated 4.4 years ago by
Kevin Blighe
★ 4.0k • written 4.4 years ago by
Marie DENIS
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: displaying the differential expression with deseq2 over 4X2 samples with the in
by
Martijn
• 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns
by
alexis.weinreb
• 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in
by
James W. MacDonald
67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
jodan
• 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA?
by
jodan
• 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Awards
• All
Popular Question
to
shepherl
4.1k
Teacher
to
Axel Klenk
★ 1.1k
Popular Question
to
Gordon Smyth
52k
Popular Question
to
bastien_chassagnol
• 0
Popular Question
to
Maria Doyle
▴ 100
Locations
• All
United States,
3 hours ago
United States,
5 hours ago
United States,
5 hours ago
Pittsburgh, United States,
5 hours ago
United States,
5 hours ago
Traffic: 515 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6